README.rdoc - README for BioRuby

The above statement is limited to this file. See below about BioRuby's
copyright and license.

++

BioRuby

Copyright (C) 2001-2011 Toshiaki Katayama <k@bioruby.org>

BioRuby is an open source Ruby library for developing bioinformatics
software. Object oriented scripting language Ruby has many features
suitable for bioinformatics research, for example, clear syntax to express
complex objects, regular expressions for text handling as powerful as
Perl's, a wide variety of libraries including web service etc. As the
syntax of the Ruby language is simple and very clean, we believe that it is
easy to learn for beginners, easy to use for biologists, and also powerful
enough for the software developers.

In BioRuby, you can retrieve biological database entries from flat files,
internet web servers and local relational databases. These database
entries can be parsed to extract information you need. Biological sequences
can be treated with the fulfilling methods of the Ruby's String class
and with regular expressions. Daily tools like Blast, Fasta, Hmmer and
many other software packages for biological analysis can be executed within
the BioRuby script, and the results can be fully parsed to extract the
portion you need. BioRuby supports major biological database formats and
provides many ways for accessing them through flatfile indexing, SQL, web
services etc. Various web services including KEGG API can be easily
utilized by BioRuby.

FOR MORE INFORMATION

See RELEASE_NOTES.rdoc for news and important changes in this version.

Documents in this distribution

Release notes, important changes and issues

README.rdoc

This file. General information and installation procedure.

RELEASE_NOTES.rdoc

News and important changes in this release.

KNOWN_ISSUES.rdoc

Known issues and bugs in BioRuby.

doc/RELEASE_NOTES-1.4.2.rdoc

News and incompatible changes from 1.4.1 to 1.4.2.

doc/RELEASE_NOTES-1.4.1.rdoc

News and incompatible changes from 1.4.0 to 1.4.1.

doc/RELEASE_NOTES-1.4.0.rdoc

News and incompatible changes from 1.3.1 to 1.4.0.

doc/Changes-1.3.rdoc

News and incompatible changes from 1.2.1 to 1.3.0.

doc/Changes-0.7.rd

News and incompatible changes from 0.6.4 to 1.2.1.

Tutorials and other useful information

doc/Tutorial.rd

BioRuby Tutorial.

doc/Tutorial.rd.html

HTML version of Tutorial.rd.

doc/KEGG_API.rd

Documents about KEGG API, including usage of Bio::KEGG::API.

BioRuby development

ChangeLog

History of changes.

doc/ChangeLog-before-1.4.2

changes before 1.4.2.

doc/ChangeLog-before-1.3.1

changes before 1.3.1.

README_DEV.rdoc

Describes ways to contribute to the BioRuby project, including coding
styles and documentation guidelines.

Documents written in Japanese

doc/Tutorial.rd.ja

BioRuby Tutorial written in Japanese.

doc/Tutorial.rd.ja.html

HTML version of Tutorial.rd.ja.

doc/KEGG_API.rd.ja

Japanese translation of KEGG_API.rd.

Sample codes

In sample/, There are many sample codes and demo scripts.

WWW

BioRuby's official website is at bioruby.org/. You will find links to related
resources including downloads, mailing lists, Wiki documentation etc. in
the top page.

REQUIREMENTS

Ruby 1.9.3-p0 or later, Ruby 1.9.2-p290 or later, or Ruby 1.8.7-p352 or
later is recommended.

See KNOWN_ISSUES.rdoc for Ruby version specific problems.

OPTIONAL REQUIREMENTS

Some optional libraries can be utilized to extend BioRuby's
functionality. If your needs meets the following conditions, install them
by using RubyGems, or download and install from the “Ruby Application
Archive” (RAA) at raa.ruby-lang.org/, RubyForge at rubyforge.org/, GitHub at github.com/, or the following web sites.

INSTALL by using RubyGems (recommended)

RubyGems is bundled with Ruby 1.9.1 or later. For Ruby 1.8.7 or earlier,
download and install RubyGems from rubygems.org/ .

INSTALL without RubyGems

In the bioruby source directory (such as bioruby-x.x.x/), run setup.rb as
follows:

% su
# ruby setup.rb

These simple step installs this program under the default location of Ruby
libraries. You can also install files into your favorite directory by
supplying setup.rb some options. Try “ruby setup.rb –help”.

If your operating system supports 'sudo' command (such as Mac OS
X), try the following procedure instead of the above.

% sudo ruby setup.rb

For older version users: “install.rb” is now renamed to “setup.rb”. The
options “config”, “setup”, and “install” are still available.

LICENSE

BioRuby can be freely distributed under the same terms as Ruby. See the
file COPYING (or COPYING.ja written in Japanese).

As written in the file COPYING, see the file LEGAL for files distributed
under different license. For example, setup.rb which comes from RAA:setup developed by
Minero Aoki (i.loveruby.net/en/projects/setup/)
is licensed under LGPL 2.1.

REFERENCE

If you use BioRuby in academic research, please consider citing the
following publication.